tbuckley/cabot-search huggingface dataset:
Abstract 712: Cytokine and TGF-β levels are associated with changes in cervicovaginal microbiota in a cohort of Caribbean women
Authors: Eduardo Lemuel Tosado Rodríguez, Anelisse Dominicci-Maura, Loyda Mendez, Stephanie Dorta, Josefina Romaguera, Filipa Godoy-Vitorino
Journal: Cancer Research (2022)

Abstract Recent studies suggest that the cervical microbiome can strongly influence inflammation and pre-cancerous lesion progression. However, research focused on understanding the role of microbial communities in the progression of pre-cancerous lesions to cancer in Latino women is scarce. We aimed to investigate the relationship between the cervicovaginal microbiome and inflammation while considering cervical neoplasia and HPV infection in Puerto Rican women. We collected cervical swabs and lavages from 142 participants coming to colposcopy clinics in San Juan, Puerto Rico. Genomic DNA was extracted from swabs, and 16S rDNA V4 region genes were amplified and sequenced by Illumina MiSeq. Inflammatory (IL-1β, TNFa, IFNg, IL-6), anti-inflammatory (IL-4, IL-10, TGFβ1), and trafficking (IL-8, MIP1a, MCP1, IP10) cytokines were measured from cervical lavages, using Luminex MAGPIX technology. Cytokines were related to microbes via an inflammation scoring index based on the quartile and tercile distribution of the cytokine’s concentration. IL-10 (p value= 0.0455) was significantly different when evaluating HPV risk, while IL1-β (p value= 0.0005) and INF-γ (p value= 0.0258) were significant when evaluating cervical disease. We found significant differences in diversity and composition of the microbiota among HPV risk, cervical disease, pro-inflammatory, anti-inflammatory, and trafficking cytokine abundances. The increasing concentration of IL1-β, IL-10, and INF-γ, associated with a decrease in Lactobacillus communities. While contrarily, bacteria associated with dysbiosis such as Gardnerella, Prevotella, Atopobium increased. This study also revealed that the most dominant community state types (CST) among Puerto Rican women regardless of lesion or HPV status, are CST3 and 4 featuring high diversity and anaerobic bacteria typical of vaginosis in Caucasians. These CSTs are especially abundant with ~ 90% dominance in participants with high grade disease (HGSIL) and high-risk HPV. Our study evidence that the cervical microbiota of Puerto Ricans is characteristically diverse and that the joint host-microbe interaction analyses via cytokine signaling and microbiota in pre-cancerous lesions has great translational potential. Citation Format: Eduardo Lemuel Tosado Rodríguez, Anelisse Dominicci-Maura, Loyda Mendez, Stephanie Dorta, Josefina Romaguera, Filipa Godoy-Vitorino. Cytokine and TGF-β levels are associated with changes in cervicovaginal microbiota in a cohort of Caribbean women [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 712.
Abstract 3767: Identification of regulators of epigenetic silencing of the p16INK4a gene
Authors: Toshitsugu Fujita, Hodaka Fujii
Journal: Cancer Research (2022)

Abstract Epigenetic silencing of tumor suppressor genes plays critical roles in oncogenesis. The CDKN2A/p16INK4a gene is one of the most frequently silenced tumor suppressor genes. To elucidate molecular mechanisms of maintenance of the silenced status of the p16INK4a gene, we applied the insertional chromatin immunoprecipitation (iChIP) method. The promoter region of the transcriptionally active and silenced alleles of the p16INK4a gene were tagged with a bacterial DNA-binding protein LexA and its binding elements. Subsequently, the promoter regions were affinity purified with antibody against a tag fused with LexA. Proteins more or less abundantly associated with the silenced promoter were identified by stable isotope labeling using amino acids in cell culture (SILAC), one of quantitative mass spectrometry methods. Knock-down experiments of the identified enzymes revealed essential components of maintenance of epigenetic silencing. The essential enzymes can be good targets of development of drugs reactivating expression of the silenced tumor suppressor genes in cancers. We are currently performing drug discovery research to identify small molecules that bind and inhibit those candidate drug target enzymes. Our locus-specific ChIP technology consisting of iChIP and the engineered DNA-binding molecule-mediated ChIP (enChIP) method is a powerful tool to identify novel drug targets for development of drugs regulating gene expression in intractable diseases. Citation Format: Toshitsugu Fujita, Hodaka Fujii. Identification of regulators of epigenetic silencing of the p16INK4a gene [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3767.
Gastroesophageal reflux disease combined with Oddi sphincter dysfunction: control of health-related quality of life in patients
Authors: L.M. Mosiychuk, L.V. Demeshkina, E.V. Zigalo
Journal: GASTROENTEROLOGY (2022)

Background. Due to the need to assess the impact of comorbid pathology (GERD and Oddi sphincter dysfunction), it is not possible to use such well-known specific questionnaires as the GERD Health-Related Quality of Life Questionnaire, the Quality of Life in Reflux and Dyspepsia and others. The purpose: to study Health-Related Quality of Life (HRQoL) before and after treatment in patients with GERD, combined with dysfunction of the sphincter of Oddi, using Short Form Health Status Survey (SF-36) and the self-developed specific questionnaire. Materials and methods. 30 patients with comorbid diseases GERD and Oddi’s sphincter dysfunction were studied. SF-36 and the self-developed specific questionnaire were used. Results. The specific questionnaire for patients with gastoesophageal reflux disease combined with Sphincter of Oddi dysfunction was worked out. The evaluation of the questionnaire (patients comprehensiveness of questions, timesuming etc.) was explored. Using SF-36, it was significant improvement of HRQoL for all scales after treatment compared with initial data: physical functioning (PF, (77,1±2,0) versus (71,4±2,2)), role-physical functioning (RP, (52,1±5,0) versus (30,6±2,4)), bodily pain (BP, (65,8±1,2) versus (48,7±2,1)), social functioning (SF, (69,5±2,0) versus (50,8±2,1)), mental health (MH, (68,5±2,1) versus (49,8±1,8)), role emotional (RE, (65,2±4,7) versus (35,8±3,7)), vitality (VT, (63,3±2,1) versus (43,2±2,2)), general health (GH, (58,1±2,4) versus (46,1±1,7) points). All patients had decreased HRQoL due to comorbid GERD and sphincter dysfunction Oddi. Moderate or significant disorders of activity and rhythm of life due to these diseases was revealed, but after treatment there was an improvement in significant HRQoL in all patients, in addition to psycho-emotional perception of their diseases became more positive. Conclusions. All patients had decreased HRQoL due to comorbid GERD and sphincter dysfunction Oddi, and it improved after treatment in most of patients.
Abstract 5731: Structure-based development of a novel MYC inhibitor for neuroendocrine prostate cancer
Authors: Jane Foo, Anh-Tien Ton, Kriti Singh, Fuqiang Ban, Helene Morin, Joseph Lee, Eric LeBlanc, Nada Lallous, Artem Cherkasov
Journal: Cancer Research (2022)

Abstract Background: MYC oncoproteins are important drivers of human cancers. More specifically, NMYC is amplified and overexpressed in neuroendocrine prostate cancer (NEPC). NMYC elicits its oncogenic effects by forming a heterodimer with MAX. This complex binds to regulating elements and activates the transcription of MYC target genes that play roles in tumor growth and progression. It is well known that members of the MYC family of proteins make compelling targets for cancer treatments. However, to this date, no tangible drug candidates have been developed into the clinics for MYC. In previous studies utilizing a rational computer-aided drug discovery (CADD) approach, we identified VPC-70551 as our most active hit. Subsequent optimization with the VPC-70551 scaffold has led to the identification of a new series of compounds. Using in silico drug screening followed by functional validation, we identified a small molecule inhibitor, VPC-70619, that exhibits higher microsomal stability and is better absorbed and tolerated orally than most MYC inhibitors described in the literature. Method: We used a transcriptional reporter assay to determine the effect of VPC-70619 on MYC-mediated transcription. To validate on-target effect, we evaluated the effect of VPC-70619 treatment on MYC-positive (LASCPC-01, NCIH660, LNCaP N-MYC, 22Rv1 N-MYC) and MYC-negative (HO15.19) cancer cells. We also evaluated the effect of VPC-70619 on MYC/MAX interaction by PLA and on DNA binding by BLI. The direct binding between recombinant MYC/MAX protein complex and VPC-70619 was evaluated by MST. Results: VPC-70619 inhibited MYC transcriptional activity in dose dependent manner and the proliferation of MYC-positive cell lines. VPC-70619 did not interfere with MYC/MAX interaction however it blocked the complex interaction with DNA. We confirmed the direct binding of VPC-70619 to the purified MYC/MAX complex by using MST. Conclusion: This project presents the identification of a new MYC inhibitor that blocks the transcriptional activity of this oncogene and elucidates the molecular mechanism of action of this inhibitor. Our findings help prelude the development and discovery of more effective treatments for NEPC patients. Citation Format: Jane Foo, Anh-Tien Ton, Kriti Singh, Fuqiang Ban, Helene Morin, Joseph Lee, Eric LeBlanc, Nada Lallous, Artem Cherkasov. Structure-based development of a novel MYC inhibitor for neuroendocrine prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5731.
Abstract 1817: EG-011 is a first-in-class Wiskott-Aldrich syndrome protein (WASp) activator with anti-tumor activity
Authors: Filippo Spriano, Laura Barnabei, Ana Maria Carrasco Del Amor, Meagan R. Tomasso, Chiara Tarantelli, Eugenia Riveiro, Natalina Pazzi, Shae B. Padrick, Susana Cristobal, Franco Cavalli, Eugenio Gaudio, Francesco Bertoni
Journal: Cancer Research (2022)

Abstract Background. Novel therapeutic targets are needed to improve the outcome of individuals with cancer. EG-011 is a small molecule with in vitro and in vivo anti-tumor activity in lymphoma and acute leukemias, but, at least so far, no activity in solid tumor models (Gaudio et al AACR 2019). Since no information was available on its target, we have now performed experiments showing that EG-011 targets WASp. Methods. Target identification: kinase screens with DiscoverX KINOMEscan, ProQinase Wildtype-Profiler; thermal proteomic profiling. Target validation: pyrene actin polymerization assay. In vitro drug treatment of cell lines followed for changes in actin filaments (F-actin) by confocal imaging with Alexa Fluor 488 Phalloidin. Results. Extensive kinome screens excluded kinases as targets of EG-011. We then applied thermal proteomic profiling to identify new protein targets interacting with EG-011. Over 3,300 proteins from the soluble proteome from the EG-011 sensitive mantle cell lymphoma cell line REC1 were analyzed and 48 possible protein targets were initially identified. Among the proteins undergoing a thermal shift, WASp was among the most highly destabilized by EG-011. Due to the pattern of expression of WASp, compatible with the anti-tumor activity observed only in hematological cancers (Gaudio et al AACR 2019), we performed further experiments to confirm the possibility that EG-011 targets WASp. One of the main functions of WASp is the regulation of actin filaments formation. Pyrene actin polymerization assays demonstrated that EG-011 activated the auto-inhibited form of WASP with strong actin polymerization. Further confirmation was obtained using confocal imaging of cell lines exposed to DMSO or EG-011 (500 nM, 5 μM) and stained for F-actin. An increase in actine polymerization was seen in EG-011 sensitive (VL51) and not in resistant (Z138) cell lines at 4, 8 and 24h with both concentrations. Conclusions. These data demonstrate that EG-011 is the “first-in-class” activator of the auto-inhibited form of WASp with selective anti-tumor activity in lymphomas. Citation Format: Filippo Spriano, Laura Barnabei, Ana Maria Carrasco Del Amor, Meagan R. Tomasso, Chiara Tarantelli, Eugenia Riveiro, Natalina Pazzi, Shae B. Padrick, Susana Cristobal, Franco Cavalli, Eugenio Gaudio, Francesco Bertoni. EG-011 is a first-in-class Wiskott-Aldrich syndrome protein (WASp) activator with anti-tumor activity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1817.
Abstract 3011: Development of mitochondrial fission inhibitors in inducing non-apoptotic cell death in triple-negative breast cancer
Authors: Saloni Malla, Shikha Kumari, David Terrero, Dayanidhi Raman, Amit K. Tiwari
Journal: Cancer Research (2022)

Abstract Triple-negative breast cancer (TNBC) is the most aggressive subtype of metastatic breast cancer with poor clinical prognosis. Presently used neoadjuvant chemotherapy against TNBC, such as taxanes, and/or anthracyclines show an initial treatment response but follows with drug resistance, tumor relapse, side effects and high proclivity to develop metastases. Recent studies point out that targeting dysregulated mitochondrial dynamics, that is now linked to the tumor initiation, progression, and metastasis in TNBC, as an effective therapeutic strategy. In particular, mitochondrial fission factors such as dynamin-related protein 1 (Drp1) is upregulated in TNBC and is known to affect mitochondrial energetics and alter metabolism which favors tumor progression. We have designed and developed small molecule inhibitors to specifically target Drp1 as a viable therapeutic strategy for metastatic TNBC (mTNBC). We recently identified a new class of structurally constrained thienopyridine (TPH) probes, and particularly a new analog TPH104c that showed higher binding affinity in silico to Drp1 as compared to Mdivi-1, a weak inhibitor of Drp1. Surface plasmon resonance studies suggest that TPH104c binds with Drp1 with high affinity. Similarly, mechanistic studies using Western blotting and immunofluorescence analysis confirmed that TPH104c significantly downregulated the levels of total and phosphorylated form of Drp1 at serine 616 in MDAMB-231 and BT-20 TNBC cells. Interestingly, Drp1 inhibition by TPH104c led to a hitherto unreported form of caspase- and reactive oxygen species (ROS)-independent non-apoptotic form of cell death. Rather than shrinking in size, or formation of apoptotic blebs which are classical features of apoptosis, TPH104c treated TNBC cells were enlarged, rounded, and swollen in size. These cells eventually lost their proliferative ability and were significantly less confluent than control cells. Additionally, in TPH104c-treated cells, neither the mitochondrial membrane potential was lost, nor the caspases were activated as also indicated by a lack of rescue of cell death when incubated with pan-caspase inhibitor. Further studies are in progress to understand the role of Drp1 inhibition in the induction of non-apoptotic cell death which will further help to optimize an effective lead compound for the future pre-clinical development of promising anticancer agents targeting mTNBC. Citation Format: Saloni Malla, Shikha Kumari, David Terrero, Dayanidhi Raman, Amit K. Tiwari. Development of mitochondrial fission inhibitors in inducing non-apoptotic cell death in triple-negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3011.
Abstract 5443: BPI-421286: A highly potent small molecule inhibitor targeting KRASG12C mutation
Authors: Xiaoguan Zhu, Yuan Lu, Jing Guo, Dan Yan, Boyan Li, Xiaoping Chen, Haibo Chen, Hong Lan, Hao Wu, Lieming Ding, Jiabing Wang
Journal: Cancer Research (2022)

Abstract KRAS is a GTP-binding protein that links receptor tyrosine kinase activation to intracellular signaling. Mutation of KRAS favors the GTP-bound active state and constitutive activation of downstream effects. KRASG12C mutation has been identified as an oncogenic driver of tumorigenesis, which is found in approximately 14% of lung cancer, 4% of colorectal (CRC), and 1-3% of other solid tumors. Herein, we report BPI-421286, a highly potent and selective covalent small molecular KRASG12C inhibitor. In vitro, BPI-421286 showed a high Kinact/Ki value (256,000 M-1 s-1), and inhibited KRAS-GTP/GDP exchange with a lower IC50 (55 nM). In cell-based assays, BPI-421286 suppressed proliferation of KRASG12C mutant cell lines with sub-nanomolar potency, but did not affect cell lines with wide type or non-G12C KRAS mutations. BPI-421286 also inhibited phospho-ERK in MIA PaCa-2 cell with a low IC50 value (2.9 nM). In vivo, daily oral administration of 3-100 mg/kg BPI-421286 led to tumor growth suppression or regression in multiple KRASG12C mutant xenograft or PDX models of NSCLC, CRC and PDAC. The in vivo PKPD in MIA PaCa-2 xenograft model showed that durable pERK inhibition can be achieved without continuous drug exposure, featuring BPI-421286 as a covalent, non-reversible KRAS inhibitor. Combining BPI-421286 with several targeted agents, including a SHP2 inhibitor BPI-442096 and a CDK4/6 inhibitor BPI-16350, demonstrated enhanced tumor growth inhibition compared to either agent alone. Notably, for the acquired resistance mutations that are clinically observed after KRASG12C inhibitor treatment, such as G12C/H95D, G12C/H95Q, G12C/R68S and G12C/Y96C, BPI-421286 also exhibited strong inhibitory activities, suggesting that BPI-421286 could overcome the acquired resistance of currently approved KRASG12C inhibitors. Taken together, BPI-421286 is a highly potent and selective KRASG12C inhibitor, with favorable ADME properties and wide therapeutic index in pre-clinical toxicology studies. BPI-421286 is currently in Phase 1 clinical study. Citation Format: Xiaoguan Zhu, Yuan Lu, Jing Guo, Dan Yan, Boyan Li, Xiaoping Chen, Haibo Chen, Hong Lan, Hao Wu, Lieming Ding, Jiabing Wang. BPI-421286: A highly potent small molecule inhibitor targeting KRASG12C mutation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5443.
Abstract 3241: IC50-Seeding Density Slope (ISDS)-measurement as a standardized methodology for assessing anti-cancer therapeutic activity <i>in vitro</i>
Authors: Ujwal Punyamurtula, Shengliang Zhang, Thomas Brown, Arielle De La Cruz, Alexander Raufi, Jillian Strandberg, Lindsey Carlsen, Lanlan Zhou, Wafik El-Deiry
Journal: Cancer Research (2022)

Abstract The 50% inhibitory concentration (IC50) is a widely used measure of how effective a given anti-cancer therapeutic is at reducing cancer cell viability in vitro. It is known that IC50 of a given therapeutic agent is dependent on the seeding density of the treated cells (in that more densely-seeded cells tend to be more resistant to therapeutic agents). We performed experiments using the CellTiter Glo cell viability assay to assess the cytotoxicity of various chemotherapeutic drugs towards various cancer cell lines. To elucidate the role the extracellular environment of densely-seeded cells plays in cancer cell chemoresistance, we tested conditioned media from cells cultured at high density on cells seeded at low densities. The resulting impact on the IC50 of the low-density cells was determined. The IC50 of the various therapeutic agents tested was cell density-dependent in each cancer cell line examined. Based on this analysis, we propose the IC50-seeding density slope (ISDS), which relates seeding density to the effectiveness of a drug and that we believe could be a standardized quantitative measurement of how a given cancer cell line responds to a given therapeutic treatment. Our results from the conditioned media experiments consistently indicated that the environment of densely-seeded tumor cells conferred chemoresistance to sparsely-seeded cells, suggesting that extracellular cytokines and growth factors may be involved in density-dependent chemoresistance mechanisms. We are currently exploring the effect of serum deprivation on in vitro chemoresistance, in order to further understand how the presence of extracellular nutrients impacts observed IC50 trends. In addition, we are examining the role that cell-cell contact, integrin and FGF signaling pathways play in giving rise to density-dependent chemoresistance. Moreover, to analyze the manner in which conditioned media gives rise to chemoresistance and how this effect relates to intracellular survival pathways, we are performing cytokine profiling experiments. Overall, we describe density-dependent IC50 variations as a hallmark of cancer cells and propose that ISDS may serve as a standardized method of assessing chemosensitivity. Citation Format: Ujwal Punyamurtula, Shengliang Zhang, Thomas Brown, Arielle De La Cruz, Alexander Raufi, Jillian Strandberg, Lindsey Carlsen, Lanlan Zhou, Wafik El-Deiry. IC50-Seeding Density Slope (ISDS)-measurement as a standardized methodology for assessing anti-cancer therapeutic activity in vitro [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3241.
Sequential Stem Cell–Kidney Transplantation in Schimke Immuno-osseous Dysplasia
Authors: Alice Bertaina, Paul C. Grimm, Kenneth Weinberg, Robertson Parkman, Karen M. Kristovich, Giulia Barbarito, Elizabeth Lippner, Girija Dhamdhere, Vasavi Ramachandran, Jordan M. Spatz, Sahar Fathallah-Shaykh, T. Prescott Atkinson, Amira Al-Uzri, Geraldine Aubert, Kim van der Elst, Sean G. Green, Rajni Agarwal, Priscila F. Slepicka, Ami J. Shah, Maria G. Roncarolo, Amy Gallo, Waldo Concepcion, David B. Lewis
Journal: New England Journal of Medicine (2022)

Lifelong immunosuppression is required for allograft survival after kidney transplantation but may not ultimately prevent allograft loss resulting from chronic rejection. We developed an approach that attempts to abrogate immune rejection and the need for post-transplantation immunosuppression in three patients with Schimke immuno-osseous dysplasia who had both T-cell immunodeficiency and renal failure. Each patient received sequential transplants of αβ T-cell-depleted and CD19 B-cell-depleted haploidentical hematopoietic stem cells and a kidney from the same donor. Full donor hematopoietic chimerism and functional ex vivo T-cell tolerance was achieved, and the patients continued to have normal renal function without immunosuppression at 22 to 34 months after kidney transplantation. (Funded by the Kruzn for a Kure Foundation.).